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- EMDB-7476: Cdc48-Npl4 complex in the presence of ATP-gamma-S -

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Basic information

Entry
Database: EMDB / ID: 7476
TitleCdc48-Npl4 complex in the presence of ATP-gamma-S
Map dataprimary map
SampleCdc48-Npl4/Ufd1 complex:
Npl4 / Putative cell division control protein / (ligand) x 3
Function / homologyNPL4, zinc-binding putative / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48), N-terminal domain / ATPase family associated with various cellular activities (AAA) / MPN domain / Ubiquitin-like domain superfamily / CDC48 domain 2-like superfamily / P-loop containing nucleoside triphosphate hydrolase / Nuclear protein localization protein 4 ...NPL4, zinc-binding putative / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48), N-terminal domain / ATPase family associated with various cellular activities (AAA) / MPN domain / Ubiquitin-like domain superfamily / CDC48 domain 2-like superfamily / P-loop containing nucleoside triphosphate hydrolase / Nuclear protein localization protein 4 / Vps4 oligomerisation, C-terminal / Aspartate decarboxylase-like domain superfamily / Nuclear pore localisation protein NPL4, C-terminal / Vps4 C terminal oligomerisation domain / AAA ATPase, CDC48 family / ATPase, AAA-type, conserved site / NPL4 family / ATPase, AAA-type, core / AAA+ ATPase domain / CDC48, N-terminal subdomain / AAA-protein family signature. / MPN domain profile. / NPL4 family, putative zinc binding region / establishment of endoplasmic reticulum localization involved in endoplasmic reticulum polarization at cell division site / sterol regulatory element binding protein cleavage / mitotic sister chromatid separation / mitotic spindle midzone / molecular adaptor activity / mitotic spindle disassembly / protein localization to Golgi apparatus / ubiquitin-dependent protein catabolic process / hydrolase activity / nuclear chromatin / cell division / ATP binding / cytoplasm / Uncharacterized protein / Putative cell division control protein
Function and homology information
SourceChaetomium thermophilum (fungus) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsingle particle reconstruction / cryo EM / 4.3 Å resolution
AuthorsKim KH / Bodnar NO / Walz T / Rapoport TA
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4.
Authors: Nicholas O Bodnar / Kelly H Kim / Zhejian Ji / Thomas E Wales / Vladimir Svetlov / Evgeny Nudler / John R Engen / Thomas Walz / Tom A Rapoport
Validation ReportPDB-ID: 6chs

SummaryFull reportAbout validation report
DateDeposition: Feb 22, 2018 / Header (metadata) release: Mar 7, 2018 / Map release: Jul 4, 2018 / Last update: Jul 18, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6chs
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7476.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.065897405 - 0.16063109
Average (Standard dev.)0.0005993301 (0.005306914)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.0.0.
Limit255.255.255.
Spacing256256256
CellA=B=C: 332.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0660.1610.001

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Supplemental data

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Sample components

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Entire Cdc48-Npl4/Ufd1 complex

EntireName: Cdc48-Npl4/Ufd1 complex / Number of components: 6

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Component #1: cellular-component, Cdc48-Npl4/Ufd1 complex

Cellular-componentName: Cdc48-Npl4/Ufd1 complex / Recombinant expression: No
SourceSpecies: Chaetomium thermophilum (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Npl4

ProteinName: Npl4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 73.880391 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Putative cell division control protein

ProteinName: Putative cell division control protein / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 90.432516 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #5: ligand, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.523247 kDa

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Component #6: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/ml / pH: 7.5
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500. X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200.0 - 2800.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 9299

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 91883
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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